LAMMPS (28 Jul 2021)
  using 1 OpenMP thread(s) per MPI task
units           lj
atom_style      full
boundary p p p

special_bonds lj/coul 1 1 1
newton on on

# save an extra atom type for bond particles
read_data data.chain
Reading data file ...
  orthogonal box = (0.0000000 0.0000000 0.0000000) to (10.000000 10.000000 10.000000)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  3000 atoms
  reading velocities ...
  3000 velocities
  scanning bonds ...
  1 = max bonds/atom
  reading bonds ...
  2700 bonds
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    1        1        1       
  special bond factors coul:  1        1        1       
     2 = max # of 1-2 neighbors
     2 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.013 seconds

neighbor        2.0 bin
neigh_modify    every 10 check yes

bond_style      harmonic
bond_coeff      * 225.0 0.85

comm_modify vel yes
comm_modify cutoff 3.6

# must use pair hybrid, since srp bond particles
# do not interact with other atoms types
pair_style      hybrid dpd 1.0 1.0 373692 srp 0.8 1 mid
pair_coeff      1 1 dpd 60.0 4.5 1.0
pair_coeff      1 2 none
pair_coeff      2 2 srp 100.0

# auto normalization of thermo quantities is turned off by pair srp
# just divide by natoms
variable        natoms equal count(all)
variable        nPotEng equal c_thermo_pe/v_natoms

thermo 50
thermo_style custom step temp pe v_nPotEng press atoms v_natoms lx ly lz

fix  1 all nve
timestep        0.01

#restart 500	mid-run-*.restart

run          1000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- @Article{Sirk2012
 author = {T. Sirk and Y. Sliozberg and J. Brennan and M. Lisal and J. Andzelm},
 title = {An enhanced entangled polymer model for dissipative particle dynamics},
 journal = {J.~Chem.~Phys.},
 year =    2012,
 volume =  136,
 pages =   {134903}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Using type 2 for bond particles
Thermo normalization turned off by pair srp (src/MISC/pair_srp.cpp:486)
Neighbor list info ...
  update every 10 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 3
  ghost atom cutoff = 3.6
  binsize = 1.5, bins = 7 7 7
  3 neighbor lists, perpetual/occasional/extra = 3 0 0
  (1) pair dpd, perpetual, skip from (3)
      attributes: half, newton on
      pair build: skip
      stencil: none
      bin: none
  (2) pair srp, perpetual, skip from (3)
      attributes: half, newton on
      pair build: skip
      stencil: none
      bin: none
  (3) neighbor class addition, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
Removed/inserted 0/2700 bond particles. (src/MISC/fix_srp.cpp:250)
Per MPI rank memory allocation (min/avg/max) = 21.70 | 21.70 | 21.70 Mbytes
Step Temp PotEng v_nPotEng Press Atoms v_natoms Lx Ly Lz 
       0   0.98262092    31772.336    10.590779    60.690437     5700         3000           10           10           10 
      50   0.99678169     31789.37    10.596457    61.967133     5700         3000           10           10           10 
     100     1.016953    31770.946    10.590315    61.808425     5700         3000           10           10           10 
     150    1.0151677    31737.965    10.579322    61.034423     5700         3000           10           10           10 
     200   0.99241972    31766.458    10.588819     60.99902     5700         3000           10           10           10 
     250    1.0101747    31816.098    10.605366    61.484391     5700         3000           10           10           10 
     300    1.0058287     31824.98    10.608327    60.656545     5700         3000           10           10           10 
     350    1.0093409    31839.963    10.613321    61.485931     5700         3000           10           10           10 
     400     1.029692     31713.44    10.571147    61.442428     5700         3000           10           10           10 
     450    1.0292264    31739.234    10.579745    61.026996     5700         3000           10           10           10 
     500    1.0141131    31796.032    10.598677    61.099407     5700         3000           10           10           10 
     550   0.99860738    31887.879    10.629293    61.412249     5700         3000           10           10           10 
     600    1.0104436    31830.675    10.610225    60.725018     5700         3000           10           10           10 
     650    1.0060939    31871.441    10.623814     61.12217     5700         3000           10           10           10 
     700    1.0394405     31724.09    10.574697    60.652294     5700         3000           10           10           10 
     750    1.0094386    31827.328    10.609109    61.274573     5700         3000           10           10           10 
     800   0.99986353    31777.205    10.592402    60.652922     5700         3000           10           10           10 
     850    0.9762615    31752.585    10.584195    61.448972     5700         3000           10           10           10 
     900   0.99324534    31794.723    10.598241    61.191199     5700         3000           10           10           10 
     950    1.0139717    31719.123    10.573041    61.876053     5700         3000           10           10           10 
    1000   0.99850758    31774.801      10.5916    60.960607     5700         3000           10           10           10 
Deleted 2700 atoms, new total = 3000
Loop time of 6.54135 on 1 procs for 1000 steps with 3000 atoms

Performance: 132082.911 tau/day, 152.874 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 4.5403     | 4.5403     | 4.5403     |   0.0 | 69.41
Bond    | 0.030682   | 0.030682   | 0.030682   |   0.0 |  0.47
Neigh   | 1.7065     | 1.7065     | 1.7065     |   0.0 | 26.09
Comm    | 0.20647    | 0.20647    | 0.20647    |   0.0 |  3.16
Output  | 0.00084543 | 0.00084543 | 0.00084543 |   0.0 |  0.01
Modify  | 0.034479   | 0.034479   | 0.034479   |   0.0 |  0.53
Other   |            | 0.022      |            |       |  0.34

Nlocal:        3000.00 ave        3000 max        3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:        12269.0 ave       12269 max       12269 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:         0.00000 ave           0 max           0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 0
Ave neighs/atom = 0.0000000
Ave special neighs/atom = 1.8000000
Neighbor list builds = 21
Dangerous builds = 0

#write_restart   end-run.restart
Total wall time: 0:00:06
